itkDiffusionTensor3DReconstructionImageFilter.h

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/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkDiffusionTensor3DReconstructionImageFilter_h
#define itkDiffusionTensor3DReconstructionImageFilter_h

#include "itkImageToImageFilter.h"
#include "itkSpatialObject.h"
#include "itkDiffusionTensor3D.h"
#include "vnl/vnl_matrix.h"
#include "vnl/vnl_vector_fixed.h"
#include "vnl/vnl_matrix_fixed.h"
#include "vnl/algo/vnl_svd.h"
#include "itkVectorContainer.h"
#include "itkVectorImage.h"

namespace itk
{
template< typename TReferenceImagePixelType,
          typename TGradientImagePixelType = TReferenceImagePixelType,
          typename TTensorPixelType = double,
          typename TMaskImageType = Image<unsigned char, 3> >
class ITK_TEMPLATE_EXPORT DiffusionTensor3DReconstructionImageFilter:
  public ImageToImageFilter< Image< TReferenceImagePixelType, 3 >,
                             Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
{
public:

  using Self = DiffusionTensor3DReconstructionImageFilter;
  using Pointer = SmartPointer< Self >;
  using ConstPointer = SmartPointer< const Self >;
  using Superclass = ImageToImageFilter< Image< TReferenceImagePixelType, 3 >,
                              Image< DiffusionTensor3D< TTensorPixelType >, 3 > >;

  itkNewMacro(Self);

  itkTypeMacro(DiffusionTensor3DReconstructionImageFilter,
               ImageToImageFilter);

  using ReferencePixelType = TReferenceImagePixelType;

  using GradientPixelType = TGradientImagePixelType;

  using TensorPixelType = DiffusionTensor3D< TTensorPixelType >;

  using ReferenceImageType = typename Superclass::InputImageType;

  using TensorImageType = Image< TensorPixelType, 3 >;

  using OutputImageType = TensorImageType;

  using OutputImageRegionType = typename Superclass::OutputImageRegionType;

  using GradientImageType = Image< GradientPixelType, 3 >;

  using GradientImagesType = VectorImage< GradientPixelType, 3 >;

  using MaskSpatialObjectType = SpatialObject<3>;

  using MaskImageType = TMaskImageType;

  using TensorBasisMatrixType = vnl_matrix_fixed< double, 6, 6 >;

  using CoefficientMatrixType = vnl_matrix< double >;

  using GradientDirectionType = vnl_vector_fixed< double, 3 >;

  using GradientDirectionContainerType = VectorContainer< unsigned int,
                           GradientDirectionType >;

  void AddGradientImage(const GradientDirectionType &, const GradientImageType *image);
  const GradientImageType *GetGradientImage(unsigned index) const;

  void SetGradientImage(GradientDirectionContainerType *,
                        const GradientImagesType *image);

  void SetReferenceImage(ReferenceImageType *referenceImage)
  {
    if ( m_GradientImageTypeEnumeration == GradientIsInASingleImage )
      {
      itkExceptionMacro(<< "Cannot call both methods:"
                        << "AddGradientImage and SetGradientImage. Please call only one of them.");
      }

    this->ProcessObject::SetNthInput(0, referenceImage);

    m_GradientImageTypeEnumeration = GradientIsInManyImages;
  }

  virtual ReferenceImageType * GetReferenceImage()
  { return ( static_cast< ReferenceImageType * >( this->ProcessObject::GetInput(0) ) ); }

  virtual GradientDirectionType GetGradientDirection(unsigned int idx) const
  {
    if ( idx >= m_NumberOfGradientDirections )
      {
      itkExceptionMacro(<< "Gradient direction " << idx << "does not exist");
      }
    return m_GradientDirectionContainer->ElementAt(idx + 1);
  }

  void SetMaskImage(MaskImageType *maskImage);

  void SetMaskSpatialObject(MaskSpatialObjectType *maskSpatialObject);


  itkSetMacro(Threshold, ReferencePixelType);
  itkGetConstMacro(Threshold, ReferencePixelType);

  itkSetMacro(BValue, TTensorPixelType);
#ifdef GetBValue
#undef GetBValue
#endif
  itkGetConstReferenceMacro(BValue, TTensorPixelType);

#ifdef ITK_USE_CONCEPT_CHECKING
  // Begin concept checking
  itkConceptMacro( ReferenceEqualityComparableCheck,
                   ( Concept::EqualityComparable< ReferencePixelType > ) );
  itkConceptMacro( TensorEqualityComparableCheck,
                   ( Concept::EqualityComparable< TensorPixelType > ) );
  itkConceptMacro( GradientConvertibleToDoubleCheck,
                   ( Concept::Convertible< GradientPixelType, double > ) );
  itkConceptMacro( DoubleConvertibleToTensorCheck,
                   ( Concept::Convertible< double, TensorPixelType > ) );
  itkConceptMacro( GradientReferenceAdditiveOperatorsCheck,
                   ( Concept::AdditiveOperators< GradientPixelType, GradientPixelType,
                                                 ReferencePixelType > ) );
  itkConceptMacro( GradientReferenceAdditiveAndAssignOperatorsCheck,
                   ( Concept::AdditiveAndAssignOperators< GradientPixelType,
                                                          ReferencePixelType > ) );

  itkConceptMacro( ReferenceOStreamWritableCheck,
                   ( Concept::OStreamWritable< ReferencePixelType > ) );
  itkConceptMacro( TensorOStreamWritableCheck,
                   ( Concept::OStreamWritable< TensorPixelType > ) );
  // End concept checking
#endif

protected:
  DiffusionTensor3DReconstructionImageFilter();
  ~DiffusionTensor3DReconstructionImageFilter() override = default;
  void PrintSelf(std::ostream & os, Indent indent) const override;

  void ComputeTensorBasis();

  void BeforeThreadedGenerateData() override;

  void DynamicThreadedGenerateData(const OutputImageRegionType & outputRegionForThread) override;

  void VerifyPreconditions() ITKv5_CONST override;

  typedef enum {
    GradientIsInASingleImage = 1,
    GradientIsInManyImages,
    Else
    } GradientImageTypeEnumeration;

private:

  /* Tensor basis coeffs */
  TensorBasisMatrixType m_TensorBasis;

  CoefficientMatrixType m_BMatrix;

  GradientDirectionContainerType::Pointer m_GradientDirectionContainer;

  unsigned int m_NumberOfGradientDirections;

  unsigned int m_NumberOfBaselineImages;

  ReferencePixelType m_Threshold;

  TTensorPixelType m_BValue;

  GradientImageTypeEnumeration m_GradientImageTypeEnumeration;

  bool m_MaskImagePresent;
};
}

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkDiffusionTensor3DReconstructionImageFilter.hxx"
#endif

#endif